From 6371fcc6a1ddddb3deae2d5fb9e5712192bf55b0 Mon Sep 17 00:00:00 2001 From: Michael Osthege Date: Fri, 20 Mar 2020 17:13:37 +0100 Subject: [PATCH 1/4] add test for xarray input to sample_posterior_predictive --- pymc3/tests/test_sampling.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/pymc3/tests/test_sampling.py b/pymc3/tests/test_sampling.py index 8d1bf00bd4..48a998ab55 100644 --- a/pymc3/tests/test_sampling.py +++ b/pymc3/tests/test_sampling.py @@ -22,6 +22,7 @@ import mock import numpy.testing as npt +import arviz as az import pymc3 as pm import theano.tensor as tt from theano import shared @@ -880,3 +881,23 @@ def test_point_list_arg_bug_spp(self, point_list_arg_bug_fixture): var_names=['d'] ) + def test_sample_from_xarray_prior(self, point_list_arg_bug_fixture): + pmodel, trace = point_list_arg_bug_fixture + + with pmodel: + prior = pm.sample_prior_predictive(samples=20) + idat = az.from_pymc3(trace, prior=prior) + with pmodel: + pp = pm.sample_posterior_predictive( + idat.prior, + var_names=['d'] + ) + + def test_sample_from_xarray_posterior(self, point_list_arg_bug_fixture): + pmodel, trace = point_list_arg_bug_fixture + idat = az.from_pymc3(trace) + with pmodel: + pp = pm.sample_posterior_predictive( + idat.posterior, + var_names=['d'] + ) From 796c9bbad1565ffc259b9eee5f88f57ffa7ffe27 Mon Sep 17 00:00:00 2001 From: Michael Osthege Date: Fri, 20 Mar 2020 17:21:48 +0100 Subject: [PATCH 2/4] support xarray.Dataset in sample_posterior_predictive + closes #3828 --- RELEASE-NOTES.md | 1 + pymc3/sampling.py | 24 +++++++++++++++++++++--- 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/RELEASE-NOTES.md b/RELEASE-NOTES.md index 56622eb903..802f40f816 100644 --- a/RELEASE-NOTES.md +++ b/RELEASE-NOTES.md @@ -8,6 +8,7 @@ - `DEMetropolisZ`, an improved variant of `DEMetropolis` brings better parallelization and higher efficiency with fewer chains with a slower initial convergence. This implementation is experimental. See [#3784](https://github.com/pymc-devs/pymc3/pull/3784) for more info. - Notebooks that give insight into `DEMetropolis`, `DEMetropolisZ` and the `DifferentialEquation` interface are now located in the [Tutorials/Deep Dive](https://docs.pymc.io/nb_tutorials/index.html) section. - Add `fast_sample_posterior_predictive`, a vectorized alternative to `sample_posterior_predictive`. This alternative is substantially faster for large models. +- `sample_posterior_predictive` can now feed on `xarray.Dataset` - e.g. from `InferenceData.posterior`. (see [#3846](https://github.com/pymc-devs/pymc3/pull/3846)) - `SamplerReport` (`MultiTrace.report`) now has properties `n_tune`, `n_draws`, `t_sampling` for increased convenience (see [#3827](https://github.com/pymc-devs/pymc3/pull/3827)) ### Maintenance diff --git a/pymc3/sampling.py b/pymc3/sampling.py index b0f920c672..8a6784dfb0 100644 --- a/pymc3/sampling.py +++ b/pymc3/sampling.py @@ -30,6 +30,7 @@ import numpy as np import theano.gradient as tg from theano.tensor import Tensor +import xarray from .backends.base import BaseTrace, MultiTrace from .backends.ndarray import NDArray @@ -1520,9 +1521,9 @@ def sample_posterior_predictive( Parameters ---------- - trace: backend, list, or MultiTrace - Trace generated from MCMC sampling. Or a list containing dicts from - find_MAP() or points + trace: backend, list, xarray.Dataset, or MultiTrace + Trace generated from MCMC sampling, or a list of dicts (eg. points or from find_MAP()), + or xarray.Dataset (eg. InferenceData.posterior or InferenceData.prior) samples: int Number of posterior predictive samples to generate. Defaults to one posterior predictive sample per posterior sample, that is, the number of draws times the number of chains. It @@ -1556,6 +1557,23 @@ def sample_posterior_predictive( Dictionary with the variable names as keys, and values numpy arrays containing posterior predictive samples. """ + if isinstance(trace, xarray.Dataset): + # grab posterior samples for each variable + _samples = { + vn : trace[vn].values + for vn in trace.keys() + } + # make dicts + points = [] + for c in trace.chain: + for d in trace.draw: + points.append({ + vn : s[c, d] + for vn, s in _samples.items() + }) + # use the list of points + trace = points + len_trace = len(trace) try: nchain = trace.nchains From fc09a793837e7dca50db7002a94a519576fb5547 Mon Sep 17 00:00:00 2001 From: rpgoldman Date: Fri, 20 Mar 2020 13:16:55 -0500 Subject: [PATCH 3/4] Michaelosthege/issue 3828 (#2) * xarray test for fast posterior predictive sampling. * Move Dataset translation to util. The translation from xarray Dataset to a list of points was previously open-coded into sample_posterior_predictive. Pulled it out so it can be used in both spp and fast_sample_posterior_predictive. * fast_sample_posterior_predictive support for xarray traces. --- docs/source/build.out | 1059 +++++++++++++++++ .../notebooks/Prior predictive bug.ipynb | 192 +++ pymc3/distributions/posterior_predictive.py | 9 +- pymc3/sampling.py | 17 +- pymc3/tests/test_sampling.py | 9 + pymc3/util.py | 24 +- 6 files changed, 1292 insertions(+), 18 deletions(-) create mode 100644 docs/source/build.out create mode 100644 docs/source/notebooks/Prior predictive bug.ipynb diff --git a/docs/source/build.out b/docs/source/build.out new file mode 100644 index 0000000000..18180ba7ef --- /dev/null +++ b/docs/source/build.out @@ -0,0 +1,1059 @@ +sphinx-build -b html -d _build/doctrees . _build/html +Running Sphinx v2.0.1 +loading pickled environment... done +building [mo]: targets for 0 po files that are out of date +building [html]: targets for 109 source files that are out of date +updating environment: 109 added, 0 changed, 0 removed +reading sources... 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already supports ODEs +~~~~~~~~~~~~~~~~~~~~~~~~~~ +/Users/rpg/src/pymc3/docs/source/notebooks/ODE_with_manual_gradients.ipynb:1163: WARNING: Title level inconsistent: + +Model selection +~~~~~~~~~~~~~~~ +/Users/rpg/src/pymc3/docs/source/notebooks/ODE_with_manual_gradients.ipynb:1171: WARNING: Title level inconsistent: + +Other AD packages +~~~~~~~~~~~~~~~~~ +/Users/rpg/src/pymc3/docs/source/notebooks/ODE_with_manual_gradients.ipynb:980: WARNING: duplicate label generative model, other instance in /Users/rpg/src/pymc3/docs/source/notebooks/convolutional_vae_keras_advi.ipynb +/Users/rpg/src/pymc3/docs/source/notebooks/bayes_param_survival_pymc3.ipynb:1296: WARNING: duplicate label authors, other instance in /Users/rpg/src/pymc3/docs/source/notebooks/weibull_aft.ipynb +/Users/rpg/src/pymc3/docs/source/notebooks/bayesian_neural_network_advi.ipynb:75: WARNING: duplicate label generating data, other instance in /Users/rpg/src/pymc3/docs/source/notebooks/GLM-linear.ipynb 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